Sleep apnea is a common sleep disorder characterized by periodic breathing cessation and intermittent hypoxia (IH). Although previous studies have demonstrated that IH alone can influence metabolic outcomes such as body weight, it remains unclear how the timing of IH can specifically affect these outcomes. Here, we examine how pairing 10-h periods of IH to either the animals' resting phase (e.g., IH during the day) or active phase (e.g., IH during the night) differentially affects body weight, macronutrient selection, energy expenditure, respiratory exchange rate, and glucose tolerance. We find that in contrast to mice exposed to IH during the night, mice exposed to IH during the day preferentially decrease their carbohydrate intake and switch to fat metabolism. Moreover, when the IH stimulus was removed, mice that had been exposed to day IH continued to eat a minimal amount of carbohydrates and consumed a higher percentage of kilocalorie from fat for at least 5 days. These data demonstrate that food choice and substrate utilization are secondary to the timing of IH but not IH itself. Taken together, these data have key clinical implications for individuals with sleep apnea and particularly those who are also experiencing circadian disruption such as night-shift workers. Pairing repeated hypoxic episodes to a mouse's resting phase during the day preferentially decreases carbohydrate intake and results in a switch to metabolic fat oxidation. These data indicate that the timing of intermittent hypoxia should be considered when calculating sleep apnea's effects on metabolic outcomes.